Chicken skin virome analyzed by high-throughput sequencing shows a composition highly different from human skin
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Recent studies show that human skin at homeostasis is a complex ecosystem whose virome include circular DNA viruses, especially papillomaviruses and polyomaviruses. To determine the chicken skin virome in comparison with human skin virome, a chicken swabs pool sample from fifteen indoor healthy chickens of five genetic backgrounds was examined for the presence of DNA viruses by high-throughput sequencing (HTS). The results indicate a predominance of herpesviruses from the Mardivirus genus, coming from either vaccinal origin or presumably asymptomatic infection. Despite the high sensitivity of the HTS method used herein to detect small circular DNA viruses, we did not detect any papillomaviruses, polyomaviruses, or circoviruses, indicating that these viruses may not be resident of the chicken skin. The results suggest that the turkey herpesvirus is a resident of chicken skin in vaccinated chickens. This study indicates major differences between the skin viromes of chickens and humans. The origin of this difference remains to be further studied in relation with skin physiology, environment, or virus population dynamics.
KeywordsMetagenomics DNA viruses Skin Chicken Herpesviruses
We thank V. Nair for the GaHV-3 HPRS-24 strain and B. Kaufer for genomic DNA from the REV-positive-CU91 cell line. We also thank J-F. Vautherot for discussions and J. Cheval and C. Hebert (PathoQuest) for HTS reads sorting and taxonomic assignation. The authors thank F. Paillard for editing the manuscript. This study has received funding from the French Government’s Investissement d’Avenir program, Laboratoire d’Excellence “Integrative Biology of Emerging Infectious Diseases” (Grant No. ANR-10-LABX-62-IBEID).
D. Gourichon was in charge of the chicken sanitary state and housing, and helped with skin swab samplings. M. Dumarest prepared the viral DNA for HTS. S. Rémy performed the experiments to verify the presence of herpesviruses and REV DNA. C. Denesvre and M. Eloit designed the project, conducted the sequence analyses, and wrote the manuscript.